I'm designing BSP primers for DNA methylation for rat BDKRB1 gene. Since gene methylation in promoter region has a regulatory effect on gene transcription, I looked up promoter regions for the gene and I did CpG island prediction to find islands. However, no CpG islands were found in the promoter region. Moreover, BSP primer design criteria entail that the primer pair must span a gene target with maximal number of islands without containing a CpG island in primer sequence itself.

question is:

Is there a use in looking at methylation status for gene expression inside the transcribed region? does DNA methylation outside promoter region affect gene transcription/expression?

I'm designing BSP primers for DNA methylation for rat BDKRB1 gene. Since gene methylation in promoter region has a regulatory effect on gene transcription, I looked up promoter regions for the gene and I did CpG island prediction to find islands. However, no CpG islands were found in the promoter region. Moreover, BSP primer design criteria entail that the primer pair must span a gene target with maximal number of islands without containing a CpG island in primer sequence itself.

question is:

Is there a use in looking at methylation status for gene expression inside the transcribed region? does DNA methylation outside promoter region affect gene transcription/expression?

Hi Moemedawar,

As the first, are you sure that the gene expression is regulated by the promoter methylation. Methylation independent primers primer can contain a limited number of CpGs ( look at Wojdacz et al; PMID: 17289753).